I wish I was a Paleontologist

Imagine you’re a paleontologist, digging through the Sahara desert looking for dinosaur bones and you stumble, instead, upon this wondrous find:


That’s exactly what happened to Paleontologist Paul Sereno and his team back in 2000, and they have announced their findings from their excavations of this region in Northern Niger in National Geographic this week. This team unexpectedly unearthed 200 human burials on the shores of a long dried up lake, representing two very distinct cultures spanning 5000 years (between 4500 to about 9000 years ago). The image shown above is of their ‘most striking discovery’, and depicts a woman and two children, ages 5 and 8, holding hands. They also found pollen in the grave, suggesting that they may have been laid on a bed of flowers. Very cool stuff. These researchers have located the remnants of two human tribes that are thought to have lived in the Sahara during the Holocene period, when environmental factors culminated in a ‘greening’ of the desert, which attracted human inhabitants.

Here’s a video featuring an interview with Paul Sereno and some nice shots of their excavation sites. They give a really nice overview of what they have discovered about the two distinct colonies found, and how they may have lived. You can also read the whole story in National Geographic, if you’re so inclined, where you will also find a link to additional photos of the site and their excavations, which are quite amazing.

Here’s a link to the study’s paper appearing in the current issue of PLoS ONE.

From guest blogger LisaJ

Usher syndrome, Part II: A complex molecular picture

Guest Blogger Danio:

I know, I know. Friday night isn’t exactly the best time to smack you with a big messy fistful of science, but PZ will be kicking us Minions out of the house early next week, so I have to stay on schedule with these Usher posts if I’m going to get through Part IV by the time he shows me the door.

In Part I, I introduced the hereditary disease known as Usher syndrome and went over a bit of the cell biology of auditory and visual sensory cells. In this post, I’ll discuss the molecules known to be affected in Usher patients, and begin to describe what is known about their function.

As mentioned previously, variations in the clinical presentation of Usher syndrome have resulted in the creation of three clinical subtypes. Type 1 is characterized by severe to profound congenital hearing loss, balance problems, and early onset vision loss, usually beginning before the patient’s 10th birthday. The type 2 hearing loss is also congenital, but tends to be less severe. The vision loss in type 2 usually begins to occur a bit later, in the early teen years, and these patients do not present with balance problems. All three categories of symptoms–vision, hearing, and balance, are progressive, commencing in childhood or adolescence rather than at birth, in Usher type 3 patients.

Despite these differences, the specific combination of deaf-blindness, plus or minus balance defects, led researchers to predict that multiple mutations in a single gene, or perhaps in two or three genes at the most, would turn out to be responsible for the symptoms observed in all Usher patients. The advent of genetic mapping led to surprising results in this regard. To date, at least 11 different genes have been implicated in the disease, nine of which have been molecularly identified thus far. More surprising still are the natures of the proteins encoded by the identified genes. In contrast to signaling or metabolic pathways, in which a genetic defect at any point in the regulatory chain of events will adversely affect the target and result in an abnormal phenotype, the Usher proteins do not act in stepwise fashion to regulate a cellular process. What they actually do is not entirely clear at this point, but the various proteins contain functional domains known to be important for scaffolding, cell adhesion and signaling, extracellular matrix formation, and motor activity.
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AAI Convention

Sastra here, with a quick reminder to those who are going to Long Beach, California to hear PZ Myers speak at the upcoming Atheist Alliance International Convention that’s coming up for the weekend of September 25th – 28th : the discounted convention rate for the Queen Mary expires August 26th, and the rooms are starting to sell out. It looks like this will be another great big fat rollicking atheist-fest.

According to the flyer, Professor PZ Myers will be speaking on the topic “Science as an Instrument of Change:”

Atheism is a natural consequence of the scientific way of looking at the world; furthermore, the scientific perspective is ascendant. Myers will explain why the new atheism is a reasonable and predictable product of our culture, and why that should give us hope for a more secular future.

Yeah, right. Militant atheist. Let’s all go and heckle him.

In addition to PZ, Michael Newdow (the plaintiff in the suit against “under God” in the pledge) and Jeremy Hall (the plaintiff in the suit against atheist discrimination in the army) will be there, along with other luminaries such as Michael Shermer, Julia Sweeney, and a special surprise awardee for the 2008 Richard Dawkins Award.

There will, of course, be a Pharyngula meet-up at some point, wedged in among all the rest of the partying. If anyone knows of any other upcoming meetups elsewhere, or just wants to whine that PZ never comes to their ship, mention them.

The “problem” is our existence

MAJeff here, getting all gay and stuff. It’s been a pretty big year for LGBT folks in the U.S. A couple weeks ago, the state in which I live repealed a law enacted during the height of anti-miscegination activity, and is now allowing same-sex couples from anywhere to marry here. Prior to that, California joined us in offering full equality to same-sex couples. That victory may be short-lived, though. There is an effort underway to take away the right to marry. Folks here can help out by contributing to Equality California who are leading the NO ON 8 campaign.

I had to chuckle the other day when I came across this post at an LA Times blog about their meeting with the folks trying to make life worse for queer people:

The measure’s supporters are generally careful to avoid appearing anti-gay, probably because they realize that, for all the voter split on same-sex marriage, Californians generally support gay rights. They professed in our meeting to have no ill will toward gay people…until the talk went deeper.

Wait, you mean they’re lying when they say they have no problems with gay people? I’m shocked! Shocked, I say!

The LA Times writer continues:

one Prop. 8 supporter said, gay rights are not as important as children’s rights, and it’s obvious that same-sex couples who married would “recruit” their children toward homosexuality because otherwise, unable to procreate themselves, they would have no way to replenish their numbers. Even editorial writers can be left momentarily speechless, and this was one of those moments

Ah, the recruitment line, code for “They’re coming to rape your children.”

The Times blogger is right: the anti-gay folks are careful to avoid showing their true colors; they work very hard to hide the anti-gay animus that drives them. But, lurking beneath the surface of their “We only want to protect marriage” lie is a deep and abiding hatred of queer folks and our communities. Their problem isn’t that we want equal access to the same rights our heterosexual counterparts have. No, their problem is that we exist at all.

That was brought home pretty clearly in a recentletter-to-the-editor in the Boston Globe:

ENOUGH ALREADY with the Globe’s gay agenda. How many front-page stories do we have to see to know that your agenda is to promote the gay/lesbian lifestyle? The July 21 article “Bloom’s off the brick row house: Buyers picking modern high-rise over classic style” could and should have been written from the heterosexual perspective. What you’re writing about is not a gay issue, it’s a human issue, and casting the story in a manner to feature gays is inappropriate. It’s time to straighten out, and I mean that in all senses of the word.

I have my own problems with such stories–namely that they continue to put forth an image of gay men as wealthier than the general public, when there’s actually a wage-penalty attached to those of us who aren’t hetero, and, regarding marriage issues, gay parents are getting by with fewer resources than their straight counterparts (that report is specifically for CA)–but that’s not the point. The bigoted letter writer isn’t concerned with accurate presentations, he’s concerned that there are gay presentations at all. Housing issues may be universal, but the universal is particular–and it’s straight.

I’m sure some folks will trot out the, “Just because I’m against gay marriage doesn’t mean I’m anti-gay” or “just because I disagree with the homosexual lifestyle doesn’t make me a bigot.” Well, it does. What they’re saying is that they want us gone. They want us to disappear. They want gay life to cease.

When folks come out and say they’re opposed to discrimination against people but actively foster such discrimination, they’re lying. They are pro-discrimination. That goes for John McCain, too, who recently said a pro-choice running mate would be acceptable, but not a pro-gay one. He has opposed every effort at including gay people in the institutions of American life. He may not be one of the crazy-ass-type fundies, but he’s also no social moderate. He’s just a “nicer” version of the “agents of intolerance” he “denounced” 8 years ago. His policy preferences on issues related to sexuality are very similar to those of Pat Robertson and John Hagee and Pope Nazinger.

McCain, Robertson, Hagge, Nazinger, McConnell…. These folks and the organizations they lead aren’t just opponents of gay rights, but enemies of gay people. They are all pushing for a return of the institutional closet. They want us neither seen nor heard. And, as ACT-UP so accurately put it, Silence=Death. They may not always want individual gay people to die, but they want our communities to do so.

I take that back, by attempting to push us back into the closet, they do want us to die. There is no life in that miserable space.

Rare footage of a solar eclipse

Here’s an awesome video of the most recent solar eclipse that took place a couple of weeks ago. This group was lucky enough to witness the eclipse from their airplane seats! You can see the eclipse pretty much from start to finish. Wait it out until the end, because it’s an amazing view when the sun comes back out. (Posted by LisaJ).

Science and human rights

Guestblogger Sastra checking in:

A few years back the little Unitarian Universalist Fellowship in my area asked me to give a brief talk (!) on the topic of my choice. Seems they were looking for speakers, any speaker, and had noticed that I tend to talk a lot. So I considered the sorts of things that appeal to me, and the sorts of things that might appeal to them, and decided to try to see if I could put together an interesting speech on “Science and Human Rights,” based on the idea “that concepts such as human rights, democracy, and science are historically linked together through similar foundations and assumptions.” I studied and filled myself with great arguments and quotations by such luminaries as Jacob Bronowski and John Dewey, shook it all together, and ended up, as I recall, driving through a blizzard to pour my impassioned argument out on a polite and appreciative crowd of about 6 people (I think (hope) the blizzard was more of a factor there, than it being me.)

Since PZ graciously gave me permission to write on “whatever floats my boat” (unless it be kiddie porn), I’m going to drag out my old notes and give a quick condensed version of my basic theme. It’s ambitious, but I think it might be relevant to Pharyngula. One of the popular stances taken by some religious apologists recently is that the methods of science grew directly from the underlying theology of the Catholic church. You also frequently hear the popular claim that the very concept of people having rights “makes no sense” without a theistic, not to say Biblical, foundation.

I’ll try then to make the secular case: that the human-centered values and rights which we see today as universal, eternal, and even self-evident have actually grown out of our recent past – and were influenced by how we did science.
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Funnels and Tornadoes and Lightning, Oh my!

MAJeff with your morning weather.


My dad took this picture and sent it to me last weekend. It’s a cold water air funnel. I thought it was cool, so I’m sharing it

When I first saw the picture, my reaction was, “OH, NO!” A couple summers ago, my dad’s business was hit by a tornado. As he tells it, the sirens went off, so he and everyone in the building went to the central storage room because it had no windows (no basement in this building). The building starts to rumble and shake, as it tends to do when you take a direct hit from a tornado. After a bit, things start to calm down, and folks begin to leave the storage room. One person asks, “Where is it?”

“Right there,” comes the reply from another staffer who was pointing out the window as the tornado made its way through a neighboring cornfield.

They ended up with some glass from the windows embedded in the cement walls, and there was structural damage that required a new roof. A couple of employee cars were damaged or destroyed, but no one in the building was injured. The houses next door and across the street, however, were flattened. When the news crews came to visit town from the Twin Cities, they had to go to one of the local bars to find the owner of the house across the street from Dad’s business. He’d also had a house destroyed in a tornado 9 years previously.

I remember that previous tornado. I had been driving home–I was living with my parents while finishing my MA–and got into the house before we got nailed with a severe thunderstorm. Got into the house, and made my way to the basement with Mom and the pets. After it calmed down a bit, I did what rural Midwesterners do: I went to the front steps to see what was happening.

When folks talk about an eerie calm, they aren’t kidding. Above my house, I watched what turned out to be an F5 tornado forming. It touched down about a mile away, and caused massive damage. The town’s power generating station was destroyed, and I ended up staying with a friend in a neighboring town, just so I could work on my thesis in light.

I had a very strange near miss this summer, but it wasn’t a tornado. Earlier this spring, we had what seemed to me to be an unusually high level of thunderstorm activity for this area. I love thunderstorms, but I love them when I’m inside watching through the windows. I was walking to class one evening in June, when all of a sudden a tree about a hundred yards or so from me was hit by lightning. My hair was all on end, and I started to move a lot more quickly to get to my classroom. I only had one city block to go, but by the time I got to my building, it had started raining HARD and hailing. I took my shoes off so they could dry and taught barefoot that night.

At least we haven’t had any “green sky” thunderstorms yet this year. Hopefully, I’ll be in the house if we do.

Usher syndrome, Part I: an introduction to sensory perception

Guest Blogger Danio:

In my introductory post I mentioned that my research focuses on the genetics of hereditary deaf-blindness, specifically Usher syndrome. As it’s likely that many of you have never heard of it, I thought I’d kick it up a notch with some sciency posts on what we know about Usher syndrome and what we think we can contribute to the diagnosis and treatment of the disease.

Usher syndrome is a genetically recessive condition characterized by hearing impairment, usually from birth, which is due to the degeneration of sensory neurons in the inner ear, and blindness due to retinal degeneration, which begins to occur in childhood or adolescence and progresses through several decades. Additionally, some Usher patients have balance problems associated with the sensory cell loss in the ear. There is a great deal of variation in the clinical presentation of the disease, and three clinical subtypes can be classified by the severity and age of onset of the symptoms. Usher syndrome affects about 1 in 17,000 Americans, and there are a number of populations around the world where the incidence is higher due to founder effects or intermarriage.

To begin to understand the pathology of this disease, one needs to focus on the affected cell types: mechanosensory hair cells and photoreceptors. Both are highly specialized types of sensory cells, but they’re performing essentially the same function, namely receiving an environmental stimulus and converting it into an electrical signal that is transmitted to the brain for interpretation. Although the nature of the stimuli–sound and light–are quite different, they are processed in much the same way, and thus it is not surprising to find a number of structural and functional similarities between photoreceptors and hair cells.
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It’s got a good beat and you can dance to it

My first of several posts about sensory cell neurobiology will be appearing shortly. To get you warmed up, here’s a movie showing a mechanosensory hair cell responding to a low frequency sound played through the glass pipette you can see in the image. *Caution*: low frequency sound may not be appropriate for work. Earphones recommended.

Also, the Scienceblogs Survey is now open again, and will remain so until 11PM EST Friday, August 15th.